logoC.briggsae small RNAs

miR-Intess™


Summary
Preprocessing
Mapping
Composition

miR classification
miR expression
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Table
Thresholds
Families
Clusters

Alignments

candidate miRBase miRNAs

miRNAknown_randfoldOK (13 loci)

cbr-mir-245

Cloning frequencies
absoluteAF16
cbr-mir-245 3arm3
normalizedAF16
cbr-mir-245 3arm0.008
cbr-mir-245 relative cloning frequencies

block134 (miRBase cbr-mir-245) [miRNAknown_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBase cbr-mir-2450.001nono0.55/0.5522/22/1.000.0
0.0
3
0
1
0
11
5
3arm
1
nd
0.18
3
31nana
block134 hairpin
  readsmiRBase family seed
seed     -------------------------------------------------------------------UUGGUCC--------------------------------------     3miR-245
  lencloning frequencies
   AF16
cbr-miR-245     ------------------------------------------------------------------ATTGGTCCCCTCCAAGTAGCTC------------------------     223
cbriggsae     ------------TCAATGTCGAAGAGCTGCTTGCAAGGTACCTAATTGTTTGA--CTCTATTCTCAATTGGTCCCCTCCAAGTAGCTCTATTGCATTGT-------------      
celegans     -------------CAATGTTGGAGAGCTATTTGCAAGGTACCTAATTGTTTGATTATTGATTCTCAATTGGTCCCCTCCAAGTAGCTCTATTGCATTG--------------      
cbrenneri     CGAAAAAAAAATTCAATGCCGTGGAGCTGCTTGCAAGGTACCTAATTGTTTGA-AATTCATTCTCAATTGGTCCCCTCCAAGTAGCTCTATTGCATTGTGTTTGTTTGTTTG      
cjaponica     -----------------------GAGCTGTTTGCAAGGTACCTAATTGTTTGA--AATGATTCTCAATTGGTCCCCTCCAAGCAGCTC------------------------      
                             *****  ***********************      *********************** *****                              
 +++++            +++++++++++++++++++++++++++++++++++++++++  ++++++++++++++++++++++++++++++++++++++++++++             +++++NM_001087019
 +++++            +++++++++++++++++++++++++++++++++++++++++  ++++++++++++++++++++++++++++++++++++++++++++             +++++NM_011380
 -----            -----------------------------------------  --------------------------------------------             -----NM_020433
 +++++            +++++++++++++++++++++++++++++++++++++++++  ++++++++++++++++++++++++++++++++++++++++++++             +++++NM_059033
 -----            -----------------------------------------  --------------------------------------------             -----NM_080788
 -----            -----------------------------------------  --------------------------------------------             -----NM_001024857
 -----            -----------------------------------------  --------------------------------------------             -----NM_001024856
cbriggsae                 .(((((.((((((((((((((...((.(((.(((((...((  ......)).)))))))).))...))))))))))).)))))))).                  1.000 -31.90
celegans                  ((((((...(((((((((((...((.(((.(((((...((........)).)))))))).))...)))))))))))...))))))                   0.999 -31.10
cbrenneri     ((((....((((.((((((.(((((((((((((...((.(((.(((((...(( (.....))).)))))))).))...))))))))))))).)))))).)))).))))....     1.000 -41.10
cjaponica                            ((((((((((...((.(((.(((((...((  (....))).)))))))).))...))))))))))                             1.000 -23.90

cbriggsaechromosome:chrI:6757247:6757331:-1Same_strand|Intronic_non-coding|NM_001087019|nr2f2 ## Opposite_strand|Intronic_coding|NM_020433|JPH2 ## Same_strand|Intronic_coding|NM_059033|C10H11.7 ## {Repeats: no} ## {MIR: cbr-mir-245}
celeganschromosome:chrI:7887372:7887456:1intergenic ## {MIR: cel-mir-245}
cbrennerichromosome:chrUn:154227073:154227183:1intergenic
cjaponicachromosome:chrUn:65682803:65682927:-1intergenic


cbr-mir-234

Cloning frequencies
absoluteAF16
cbr-mir-234 3arm1
normalizedAF16
cbr-mir-234 3arm0.003
cbr-mir-234 relative cloning frequencies

block855 (miRBase cbr-mir-234) [miRNAknown_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBase cbr-mir-2340.002nono0.38/0.3821/21/1.000.0
0.0
1
0
1
0
16
7
3arm
1
nd
0.10
1
11nana
block855 hairpin
  readsmiRBase family seed
seed     ------------------------------------------------------------------------------------UAUUGCU------------------------------------------------     1miR-234
  lencloning frequencies
   AF16
cbr-miR-234     -----------------------------------------------------------------------------------TTATTGCTCGAGAATACCCTT-----------------------------------     211
cbriggsae     --------------ACTCTAGCAAA-----GATCAAACGGTATTCCTGAGTGAATAATAAAAATG-------AGTCCATTCTATTATTGCTCGAGAATACCCTTTGACAAGC---TGAAAAGT----------------      
cremanei     -GATGAATGGTAAGTGGTGAACCAA-----GCTCAAACGGTATTCGACGGTGAATAATAAAAATGACATTGCGACTCATTCTATTATTGCTCGAGAATACCCTTTGACACGG---TTCACCTTTTTTTTGGTATTTGTC      
celegans     CTATGTAAGTTGAAACACAAAAAAT-----GATCAAACGGTATTCCAGAGTTGATAATAAAAATG-CGTCAGTCCGCAATCTATTATTGCTCGAGAATACCCTTTGACTACTATGTGTACGTTTTTATTAG--------      
cbrenneri     ------------GAATTCATGCAACAATCAGCTCAAACGGTATTCTTTGGTTAATAATAAGGATGGCATCACGACTCATTATATTATTGCTCAAGAATACCCTTTGACAAA----TGTCGCGTGACATC----------      
cjaponica     ------------AAAAACACACCAC-----GTTCGATAGGTGTTCCAGAGTTGATAATAATCGTGCCAT--GTGCACATT-TATTATTGCTTGAGAATACCCCTCGGCAGAT---TGTGTTCTGTTTTT----------      
ppacificus     --------GATGGATTTCGAGGTCT-----GTTTAGAGGATAT---------------------------------CGATCAACTATTGCTCGAGAGATTCCATT----------------------------------      
                                    * *     * * *                                 *  *  * *******  ***    ** *                                         
 +++++              +++++++++++     +++++++++++++++++++++++++++++++++++       ++++++++++++++++++++++++++++++++++++++++   ++++++++                +++++NM_001111076
 +++++              +++++++++++     +++++++++++++++++++++++++++++++++++       ++++++++++++++++++++++++++++++++++++++++   ++++++++                +++++NM_135942
 +++++              +++++++++++     +++++++++++++++++++++++++++++++++++       ++++++++++++++++++++++++++++++++++++++++   ++++++++                +++++NM_001105037
 +++++              +++++++++++     +++++++++++++++++++++++++++++++++++       ++++++++++++++++++++++++++++++++++++++++   ++++++++                +++++NM_001078409
 +++++              +++++++++++     +++++++++++++++++++++++++++++++++++       ++++++++++++++++++++++++++++++++++++++++   ++++++++                +++++NM_028335
 +++++              +++++++++++     +++++++++++++++++++++++++++++++++++       ++++++++++++++++++++++++++++++++++++++++   ++++++++                +++++NM_021952
 +++++              +++++++++++     +++++++++++++++++++++++++++++++++++       ++++++++++++++++++++++++++++++++++++++++   ++++++++                +++++NM_182531
 -----              -----------     -----------------------------------       ----------------------------------------   --------                -----NM_012560
 -----              -----------     -----------------------------------       ----------------------------------------   --------                -----NM_070558
 -----              -----------     -----------------------------------       ----------------------------------------   --------                -----NM_016734
 +++++              +++++++++++     +++++++++++++++++++++++++++++++++++       ++++++++++++++++++++++++++++++++++++++++   ++++++++                +++++NM_006962
 +++++              +++++++++++     +++++++++++++++++++++++++++++++++++       ++++++++++++++++++++++++++++++++++++++++   ++++++++                +++++NM_003428
 +++++              +++++++++++     +++++++++++++++++++++++++++++++++++       ++++++++++++++++++++++++++++++++++++++++   ++++++++                +++++NM_001013387
 +++++              +++++++++++     +++++++++++++++++++++++++++++++++++       ++++++++++++++++++++++++++++++++++++++++   ++++++++                +++++NM_001007088
 +++++              +++++++++++     +++++++++++++++++++++++++++++++++++       ++++++++++++++++++++++++++++++++++++++++   ++++++++                +++++NM_001002954
 +++++              +++++++++++     +++++++++++++++++++++++++++++++++++       ++++++++++++++++++++++++++++++++++++++++   ++++++++                +++++NM_001127372
cbriggsae                   ....((((...     ..(((((.(((((((.(((((.(((((((..((((       ....)))).)))))))))))).))))))).)))))...))   ))......                     0.880 -26.60
cremanei      ((..((((.((((.((((((((..     ..(((((.(((((((..((((.(((((((..(((((.........))))).))))))))).)).))))))).)))))...))   )))))).....)))).))))..))     1.000 -40.40
celegans     (((.(((((.....(((((......     ..(((((.(((((((..(((.((((((((....(( ((......))))...)))))))))))..))))))).)))))......))))).....))))))))             0.875 -30.04
cbrenneri                 ....((((((.(((......(((((.(((((((((.((.((((((((..(((((.........))))).)))))))))).))))))))).)))))....    ))).))))))....               0.999 -32.00
cjaponica                 (((((((...(((     (.((((..(((((((..(((.(((((((((..((((...  ..))))..) )))))))))))..)))))))..)))).....   ))))...)))))))               0.980 -32.00
ppacificus             (((((((((((((....     ...(((..(((..                                 ..)))..)))...)))))))...))))))                                       0.667 -14.10

cbriggsaechromosome:chrII:319385:319478:1Same_strand|Intronic_coding|NM_001111076|Zfp182 ## Same_strand|Intronic_non-coding|NM_001078409|zf(c2h2)-7 ## Opposite_strand|Intronic_non-coding|NM_012560|Foxg1 ## {Repeats: no} ## {MIR: cbr-mir-234}
cremaneichromosome:chrUn:46416256:46416385:1intergenic
celeganschromosome:chrII:14466154:14466278:-1intergenic ## {MIR: cel-mir-234}
cbrennerichromosome:chrUn:164688025:164688137:-1intergenic
cjaponicachromosome:chrUn:86889440:86889545:-1intergenic
ppacificuschromosome:chrUn:142403762:142403895:1Same_strand|Boundary_coding|NM_173471 ## Same_strand|Intronic_coding|NM_001020069 ## Opposite_strand|Intronic_coding|NM_134696 ## Same_strand|Boundary_non-coding|NM_143158


cbr-mir-41

Cloning frequencies
absoluteAF16
cbr-mir-41 3arm1
normalizedAF16
cbr-mir-41 3arm0.003
cbr-mir-41 relative cloning frequencies

block972 (miRBase cbr-mir-41) [miRNAknown_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBase cbr-mir-410.001nono0.52/0.5520/21/1.000.0
0.0
1
0
1
0
22
5
3arm
1
nd
0.19
2
11nana
Clusters
Located in cluster 3: cbr-mir-36, cbr-mir-38, cbr-mir-39, cbr-mir-40, block969_novel, cel-mir-35, cbr-mir-41, cbr-mir-35
Families
Member of family miR-35/36/38/39/40/41 (seed CACCGGG): cel-mir-35, cel-mir-35, cel-mir-36, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cbr-mir-39, cbr-mir-35, cbr-mir-36, cbr-mir-40, cbr-mir-41, cbr-mir-38, block969_novel, block5129_cand
block972 hairpin
  readsmiRBase family seed
seed     ---------------------------------------------------------------------------------------CACCGGG-----------------------------------------------------     1miR-35/36/38/39/40/41
  lencloning frequencies
   AF16
      --------------------------------------------------------------------------------------TCACCGGGTGAAAAACT-CCC----------------------------------------     201
cbr-miR-41     --------------------------------------------------------------------------------------TCACCGGGTGAAAAACT-CCCA---------------------------------------     21-
cbriggsae     -------------------TGAAAGCAGGTCCCAAATGCCTTGGTGGTTTTTCGCCGTAGTGATACAACATCGAAGCCATACGATATCACCGGGTGAAAAACT-CCCAAGGTCGGGACATTTTTATTTGT-----------------      
cremanei     ---------GAAAGGTAAGTTTA-ACAGGTCCCCATGACCTTGGTAGTTTTCCGCCGCAGTGATATACCATC-AATCAAAACGATATCACCGGGTGAAAAACT-ACCAAGGTCGGGTCACCTGTCCTTTTTTCTATTCTTCCCCTTC      
celegans     GATATCAAGGTGAGTTATTTTTAAGTGGGTCCCAGAGACCTTGGTGGTTTTTCTCTGCAGTGATAGATACTTCTAACAACTCGCTATCACCGGGTGAAAAATC-ACCTAGGTCTGGAGCCTCCTGCTCTTTTTTTGCTGTT------      
cbrenneri     ---GTTCATATTTTTCATATTCA-GGGGTGGATCGGGCCTGTGCTGATTTTT-GCCGCTGTGATA---TTTCTAAGCCATG-ATTATCACCGGGCGAAAATTTGGCACAGGCCTCGTCCGCCCT-----------------------      
cjaponica     -----------------------------GGCTGGTATCCGCGATGGTGTTACACTACTGTAATG-------------------TATCACCGGGTGGAAACTT-GCA----------------------------------------      
ppacificus     ---GT------------------------------AGCTCATTGTGATTTTGCC------TAATGAGCTCTATGTGAAACGCGCAATCACCGGGTG--AATTT-GCAGTGA------------------------------------      
                                                  *  * **         * **                     ********* *  **     *                                               
 -----                   ------------------------------------------------------------------------------------ --------------------------                 -----NM_177732
 -----                   ------------------------------------------------------------------------------------ --------------------------                 -----NM_214509
 -----                   ------------------------------------------------------------------------------------ --------------------------                 -----NM_207243
 -----                   ------------------------------------------------------------------------------------ --------------------------                 -----NM_207243
 -----                   ------------------------------------------------------------------------------------ --------------------------                 -----NM_207243
 -----                   ------------------------------------------------------------------------------------ --------------------------                 -----NM_207243
 -----                   ------------------------------------------------------------------------------------ --------------------------                 -----NM_207243
 -----                   ------------------------------------------------------------------------------------ --------------------------                 -----NM_207243
 -----                   ------------------------------------------------------------------------------------ --------------------------                 -----NM_207243
 -----                   ------------------------------------------------------------------------------------ --------------------------                 -----NM_207243
 -----                   ------------------------------------------------------------------------------------ --------------------------                 -----NM_207243
 -----                   ------------------------------------------------------------------------------------ --------------------------                 -----NM_207243
 -----                   ------------------------------------------------------------------------------------ --------------------------                 -----NM_207243
 -----                   ------------------------------------------------------------------------------------ --------------------------                 -----NM_001030843
 +++++                   ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++++++++++++                 +++++NM_001101718
 +++++                   ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++++++++++++                 +++++NM_001011629
 -----                   ------------------------------------------------------------------------------------ --------------------------                 -----NM_207243
 -----                   ------------------------------------------------------------------------------------ --------------------------                 -----NM_207243
 -----                   ------------------------------------------------------------------------------------ --------------------------                 -----NM_207243
 -----                   ------------------------------------------------------------------------------------ --------------------------                 -----NM_207243
 -----                   ------------------------------------------------------------------------------------ --------------------------                 -----NM_207243
 -----                   -------------------------------------------------------------<<--------------------- --------------------------                 -----NM_171042
cbriggsae                        ((((((...(((((....(((((((..((((((((((...((((((.....(((........)))))))))..)))))))))). .))))))).))))).)))))).....                      1.000 -43.00
cremanei              ((((((........ ((((((..((.((((((((((((((((.((((...(((((((...... ..........)))))))..)))).)))))) ))))))))))))..)))))))))))).................     0.998 -51.29
celegans     ((((.(((((.((((........((..((..((..((((((.(((((((((((((((..(((((((.................))))))))))).)))))))) ))).))))))))..))..))))))...))))).))))           0.987 -47.93
cbrenneri        .................... (((((((((.(((((((((((((((((( (((...((((((   ..((........) ).))))))..)))))))))).))))))))))).)))))))))                            0.944 -57.20
cjaponica                                  .((.(((.(((((..(((((.((((.........))                   )).))))).))))).))). )).                                             1.000 -21.90
ppacificus        ..                              ...(((((((((.((..((      (..(((......((((.....)))).)))..)))..  )).)) )))))))                                         0.985 -19.40

cbriggsaechromosome:chrII:7536494:7536603:1Opposite_strand|Intronic_non-coding|NM_177732|Slc35d1 ## Opposite_strand|Intronic_coding|NM_214509|COLP1alpha ## Same_strand|Intronic_coding|NM_001101718|LOC100009540 ## Same_strand|Intronic_non-coding|NM_001011629|Mblk-1 ## {Repeats: no} ## {MIR: cbr-mir-41}
cremaneichromosome:chrUn:8778344:8778478:-1Same_strand|Intronic_coding|NM_001011005 ## Opposite_strand|Intronic_coding|NM_171042
celeganschromosome:chrII:11538198:11538337:1Opposite_strand|Intronic_coding|Y62F5A.9 ## {MIR: cel-mir-41}
cbrennerichromosome:chrUn:47821556:47821670:-1intergenic ## {SimpF: trf}
cjaponicachromosome:chrUn:117591201:117591350:-1Opposite_strand|Intronic_coding|NM_171042
ppacificuschromosome:chrUn:87745955:87746023:1Same_strand|Boundary_coding|NM_066985 ## Same_strand|Intronic_coding|NM_001110823


cbr-mir-259

Cloning frequencies
absoluteAF16
cbr-mir-259 5arm1
normalizedAF16
cbr-mir-259 5arm0.003
cbr-mir-259 relative cloning frequencies

block4075 (miRBase cbr-mir-259) [miRNAknown_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBase cbr-mir-2590.002nono0.33/0.3921/23/1.000.0
2.0
1
0
1
0
16
1
5arm
1
nd
0.22
2
11nana
block4075 hairpin
  readsmiRBase family seed
seed     -----------------------------------AAUCUCA-------------------------------------------------------------------------------------------------     1miR-259
  lencloning frequencies
   AF16
      ----------------------------------AAATCTCATCCTAATCTGGTTG---C-------------------------------------------------------------------------------     231
cbr-miR-259     ----------------------------------AAATCTCATCCTAATCTGGTT------------------------------------------------------------------------------------     21-
cbriggsae     ------------------AGTCATCGAAACGAGTAAATCTCATCCTAATCTGGTTG---CATTTTCAATACTT--TTTGCTACCGATTTGGT-TTGGGATTGGCT--TGTCTAGTATTGAC------------------      
cremanei     ----------------------------------AAATCTCATCCTAATCTGGTTGACACAACACAAGGA-----AGTGCTACCGATTTGGC-TTGGGATTG-------------------------------------      
celegans     -----GTAAGTTCGGTTCAGTCATTGAAACGAGTAAATCTCATCCTAATCTGGTAG---CATCTTTCGAAC----CTTGCCACCGATTTGGC-ATGGGATTGACT--TGTTAAATAGTGACTTTTTTCTTGC-------      
cbrenneri     TCAAAAAAGGTAAGTGATTGTCAGTGAAACGAGTTAATCTCATCCTAATCTGGTCG---CATCACAAAACTTA--CCTGCTACCGATTTGGC-TTGGGATTGACT--CGTTGAATTTTGACTATTGTCCTAGTTTTCGA      
cjaponica     ----GGTAAGCTCTGTTTTGTCAGCAATACGAGTAAATCTCATCCTAATCTGGTCGCAAAATTATCAAAATGGACAATGCTACCGGTTCGGCTTTGGGATTGACTCGTGTTTAGAACTGACACTTTCTTCC--------      
                                         ******************* *    *                *** **** ** **   ********                                           
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_080814
 +++++                  ++++++++++++++++++++++++++++++++++++++   ++++++++++++++  +++++++++++++++++ ++++++++++++  ++++++++++++++                  +++++NM_070877
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_007732
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_080804
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_080630
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_001003090
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_008331
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_001100911
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_032518
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_080801
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_009930
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_026030
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_080798
 +++++                  ++++++++++++++++++++++++++++++++++++++   ++++++++++++++  +++++++++++++++++ ++++++++++++  ++++++++++++++                  +++++NM_072417
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_201478
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_007732
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_067556
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_080803
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_080629
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_080630
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_080810
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_080680
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_212528
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_080679
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_053304
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_007742
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_001076831
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_001076831
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_030582
 +++++                  ++++++++++++++++++++++++++++++++++++++   ++++++++++++++  +++++++++++++++++ ++++++++++++  ++++++++++++++                  +++++NM_001100591
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_199214
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_131292
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_053304
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_080809
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_080807
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_199214
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_152888
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_080808
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_001003090
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_005203
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_080802
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_080811
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_000090
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_080806
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_000090
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_007729
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_001087789
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_203889
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_001087352
 +++++                  ++++++++++++++++++++++++++++++++++++++   ++++++++++++++  +++++++++++++++++ ++++++++++++  ++++++++++++++                  +++++NM_204577
 +++++                  ++++++++++++++++++++++++++++++++++++++   ++++++++++++++  +++++++++++++++++ ++++++++++++  ++++++++++++++                  +++++NM_001038742
 +++++                  ++++++++++++++++++++++++++++++++++++++   ++++++++++++++  +++++++++++++++++ ++++++++++++  ++++++++++++++                  +++++NM_080338
 +++++                  ++++++++++++++++++++++++++++++++++++++   ++++++++++++++  +++++++++++++++++ ++++++++++++  ++++++++++++++                  +++++NM_167026
 +++++                  ++++++++++++++++++++++++++++++++++++++   ++++++++++++++  +++++++++++++++++ ++++++++++++  ++++++++++++++                  +++++NM_167027
 +++++                  ++++++++++++++++++++++++++++++++++++++   ++++++++++++++  +++++++++++++++++ ++++++++++++  ++++++++++++++                  +++++NM_064380
 +++++                  ++++++++++++++++++++++++++++++++++++++   ++++++++++++++  +++++++++++++++++ ++++++++++++  ++++++++++++++                  +++++NM_141224
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_032085
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_205305
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_001087258
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_001090075
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_001105289
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_001034039
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_001105289
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_001090075
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_001046199
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_001087352
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_001011005
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_214509
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_001033832
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_001034039
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_131292
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_174634
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_009932
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_080595
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_130445
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_080800
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_007737
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_198721
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_000393
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_000393
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_001854
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_001854
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_080629
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_001080091
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_001122918
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_001122918
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_000493
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_001029897
 -----                  --------------------------------------   --------------  ----------------- ------------  --------------                  -----NM_001130103
cbriggsae                       .((((.(...((((((.(((((((..((((..((((.(   ((............  ..))).))))..)))). .))))))).)))  )))...)...))))                       1.000 -29.44
cremanei                                       .(((((((..((((..((((...(((..........     .)))..))))..)))). .))))))).                                          0.987 -16.10
celegans          (((((........((((((((.(((((((.((((((((((.((((.(((.(   ((..........    ..))).))))))).)). )))))))).)))  ))))...)))))))).....)))))            1.000 -37.62
cbrenneri     .......(((....((((.(((((...(((((((((((((((..((((..((((.(   ((............  ..))).))))..)))). .)))))))))))  )))).....))))).)))).))).........     0.995 -39.04
cjaponica         ..............((((((.(((((((((.(((((((.((.((.(((((.(((...((.((......)).))))).))))))).))...))))))).))))))))).....)))))).........             0.879 -35.00

cbriggsaechromosome:chrV:7917242:7917336:1Opposite_strand|Intronic_coding|NM_080814|COL13A1 ## Same_strand|Intronic_coding|NM_070877|ugt-42 ## Opposite_strand|Intronic_non-coding|NM_008331|Ifit1 ## Same_strand|Intronic_non-coding|NM_001100591|Rc3h2 ## {Repeats: no} ## {MIR: cbr-mir-259}
cremaneichromosome:chrUn:57576530:57576664:-1Opposite_strand|Intronic_coding|NM_001114256 ## Same_strand|Intronic_coding|NM_067581
celeganschromosome:chrV:10538991:10539107:-1intergenic ## {MIR: cel-mir-259}
cbrennerichromosome:chrUn:67725526:67725656:1intergenic
cjaponicachromosome:chrUn:47919156:47919282:-1Same_strand|Intronic_coding|NM_021343


cbr-mir-255

Cloning frequencies
absoluteAF16
cbr-mir-255 3arm1
normalizedAF16
cbr-mir-255 3arm0.003
cbr-mir-255 relative cloning frequencies

block4081 (miRBase cbr-mir-255) [miRNAknown_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBase cbr-mir-2550.001nono0.27/0.2722/22/1.000.0
0.0
1
0
1
0
16
5
3arm
1
nd
0.09
1
11nana
block4081 hairpin
  readsmiRBase family seed
seed     -------------------------------------------------------------------AACUGAA---------------------------------------------     1miR-255
  lencloning frequencies
   AF16
cbr-miR-255     ------------------------------------------------------------------AAACTGAAGAGATTTTTTACAG-------------------------------     221
cbriggsae     --------GATGTCTCTTCATTATCAGGTAAGAAATCTTTGTAGTTTTCCGCGAGTCAAC--GTGAAAACTGAAGAGATTTTTTACAGATTCCGGAGGAGCATC---------------      
cremanei     -------------------------AGGTAAGAAATCTTTGTGGTTTTCCGTGTTTAAAC--GCGAAAACTGAAGAGATTTTTTACAG-------------------------------      
celegans     CTTCAGTGGTTCGACTAAATTTTGGAGGTAAGAAATCTTTGTAGTTCTCCGTATTGTGAC--GTGAAAACTGAAGAGATTTTTTACAGACTTCACAAATTTGAAATATATTCCTGCAAG      
cbrenneri     -------------------------AGGTAAGAAATCTTTGTGGTTTTCCGTTATGAGAC--GAGAAAACTGAAGAGATTTTTTACAG-------------------------------      
cjaponica     ----------------------CTCACGCA--AATCCTGGACAGTTTACGGAGATTGAACCGGCGAAAACTGAATGTTTGTATTGAA--------------------------------      
                               * * *  **  **     ***  * *       **  * **********    * * **  *                                      
 -----        ----------------------------------------------------  ------------------------------------------               -----NM_001011629
 -----        ----------------------------------------------------  ------------------------------------------               -----NM_214466
 -----        ----------------------------------------------------  ------------------------------------------               -----NM_071851
 -----        ----------------------------------------------------  ------------------------------------------               -----NM_001003090
 -----        ----------------------------------------------------  ------------------------------------------               -----NM_152229
 -----        ----------------------------------------------------  ------------------------------------------               -----NM_131402
 -----        ----------------------------------------------------  ------------------------------------------               -----NM_070565
 -----        ----------------------------------------------------  ------------------------------------------               -----NM_214509
 -----        ----------------------------------------------------  ------------------------------------------               -----NM_070407
 -----        ----------------------------------------------------  ------------------------------------------               -----NM_001031045
 -----        ----------------------------------------------------  ------------------------------------------               -----NM_001122918
cbriggsae             ((((.((((((...(((..(((((((((((((.((((((((.(((......)  )))))))))).))))))))))))).)))....))))))))))                    1.000 -37.60
cremanei                              ..(((((((((((((.(((((((((((......))  ).)))))))).)))))))))))))..                                    1.000 -24.80
celegans     ((((((..((.....(((((((((((((((((((((((((.(((((.(((((......))  ).)).))))).)))))))))))))...))))).)))))))......))..))).)))     0.994 -31.00
cbrenneri                              ..(((((((((((((.((((((((((((....)))  ).)))))))).)))))))))))))..                                    1.000 -25.00
cjaponica                           .(((.(((  (((......((((((.(((........)))....))))))...))))))..))).                                     0.875 -10.90

cbriggsaechromosome:chrV:8908222:8908315:1Opposite_strand|Intronic_non-coding|NM_001011629|Mblk-1 ## Opposite_strand|Intronic_coding|NM_214466|COLP3alpha ## {Repeats: no} ## {MIR: cbr-mir-255}
cremaneichromosome:chrUn:141254727:141254860:1Opposite_strand|Intronic_coding|NM_072673
celeganschromosome:chrV:5440620:5440736:1intergenic ## {MIR: cel-mir-255}
cbrennerichromosome:chrUn:186086573:186086706:1intergenic
cjaponicachromosome:chrUn:104537766:104537899:-1Same_strand|Intronic_coding|NM_066158


cbr-mir-787

Cloning frequencies
absoluteAF16
cbr-mir-787 3arm1
normalizedAF16
cbr-mir-787 3arm0.003
cbr-mir-787 relative cloning frequencies

block4425 (miRBase cbr-mir-787) [miRNAknown_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBase cbr-mir-7870.002nono0.39/0.3923/23/1.000.0
0.0
1
0
1
0
12
2
3arm
1
nd
0.26
3
11nana
Families
Member of family miR-231/787 (seed AAGCUCG): cbr-mir-231, cbr-mir-787
block4425 hairpin
  readsmiRBase family seed
seed     -----------------------------------------------------------------------------------AAGCUCG-----------------------------------------------     1miR-231/787
  lencloning frequencies
   AF16
cbr-miR-787     ----------------------------------------------------------------------------------TAAGCTCGTCTTAGTTTTCCT----CT----------------------------     231
cbriggsae     -----------CCTCAAAATGGA---------------GAAGAAGGAAACTAGACAATCTTACATA-GCTCAAAATAATCTGTAAGCTCGTCTTAGTTTTCCT----CTCCTC-------------TCTAGGGA---      
cremanei     -------CTTTTTTCCACATGGATATGTGGGACCAGTGGATGAGGGAAACTAGTCGATCTCACACTAATTTGACAGAA--TGTAAGCTCGTCTTTGTTTTCCTGCATCTCTGGTCCCCCAACTTGTTCAATGGTAAG      
celegans     ----------------GGATGTAT---------CAGTGGACGAAAGATACAT-ACGATCTTACATC--TTCAAAATGGTATGTAAGCTCGTTTTAGTATCTTT----CGTCTCTGATCACATTCAATTAAGGTA---      
cjaponica     CGATAGTTTTGTGTGTGTATGGAT-----------GGGGAAGAGGGAAACATGATGGTCTCACATT--CTTAAGATGCT-TGTAAGCTCGTCTT-GTTTCCTTCTTCTTCTTCAAATGCCACTAAATTTGTG-----      
                        *** *               ** **  ** **       *** ***     *  * *     *********** ** ** *   *                       *    *           
 -----           ------------               ---------------------------- ------------------------------------    ------             --------   -----NM_001105250
 -----           ------------               ---------------------------- ------------------------------------    ------             --------   -----NM_004796
 -----           ------------               ---------------------------- ------------------------------------    ------             --------   -----NM_138970
 -----           ------------               ---------------------------- ------------------------------------    ------             --------   -----NM_001087279
 +++++           ++++++++++++               ++++++++++++++++++++++++++++ ++++++++++++++++++++++++++++++++++++    ++++++             ++++++++   +++++NM_072374
 +++++           ++++++++++++               ++++++++++++++++++++++++++++ ++++++++++++++++++++++++++++++++++++    ++++++             ++++++++   +++++NM_007496
 -----           ------------               ---------------------------- ------------------------------------    ------             --------   -----NM_001080396
 -----           ------------               ---------------------------- ------------------------------------    ------             --------   -----NM_001092981
cbriggsae                (((.....((((               (((((.(((((((((((...((((((.. .............))))))...))).)))))))).)    ))..))             ))))))).        1.000 -24.16
cremanei            .......(((..((((((.((((((((((.(((((((((((((.((.(((.((.(((((........))..  ))).)).))).))..)))))))).)))))))))))))...)).)))))).)))....     0.993 -44.80
celegans                     ((((((((         (((.(((((((((((((.. ((((.((((((((  (.......)).))))))).))))....))))))))    )))))))))).))))))..........        0.996 -43.40
cjaponica     ....(((((.(((.((((.((((.           ((((((((((((((((.((((..((.(((.(  (....)).... ))).))..)))).) ))))))))))))))))))).))))))).)))))....          0.993 -42.30

cbriggsaechromosome:chrX:5375318:5375407:-1Opposite_strand|Intronic_non-coding|NM_001105250|NRXN3 ## Same_strand|Intronic_coding|NM_072374|C33G8.2 ## Same_strand|Intronic_non-coding|NM_007496|Zfhx3 ## Opposite_strand|Intronic_coding|NM_001080396|FAM155A ## {Repeats: no} ## {MIR: cbr-mir-787}
cremaneichromosome:chrUn:33359160:33359287:1intergenic
celeganschromosome:chrX:11294635:11294736:1intergenic ## {MIR: cel-mir-787}
cjaponicachromosome:chrUn:544633:544749:1intergenic


cbr-mir-251

Cloning frequencies
absoluteAF16
cbr-mir-251 5arm4
normalizedAF16
cbr-mir-251 5arm0.010
cbr-mir-251 relative cloning frequencies

block4433 (miRBase cbr-mir-251) [miRNAknown_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBase cbr-mir-2510.001nono0.42/0.4821/24/1.000.0
1.0
4
0
1
0
16
1
5arm
1
nd
0.08
1
41nana
block4433 hairpin
  readsmiRBase family seed
seed     -------------------------UAAGUAG--------------------------------------------------------------------------------     4miR-251
  lencloning frequencies
   AF16
      ------------------------TTAAGTAGTGGTGCCGCTCTT-------------------------------------------------------------------     212
      ------------------------TTAAGTAGTGGTGCCGCTCTTAT-----------------------------------------------------------------     232
cbr-miR-251     ------------------------TTAAGTAGTGGTGCCGCTCTTATT----------------------------------------------------------------     24-
cbriggsae     -------CCCAAA-TGACATCTCGTTAAGTAGTGGTGCCGCTCTTATTAGAA--TTATCAAGTAATAAGAGTTGTTCGCTACTTAACGAGAGGAAATTTGGA----------      
cremanei     TTCTCGTTCCAAA-TAACCCCTTGTTAAGTAGTGGTGCCGCTCTTATTAG-A--ATCCAGAATAATAAGAGTCGCTCACTGCTTATCAAGGTGAAATTTGGGTTTTTGTGAG      
celegans     ATTCAACTTTCAA-TGACCCCTTGTTAAGTAGTGGTGCCGCTCTTATTAG-G--TTGAAAAGTAATAAGAGTAGTTCACTACTTATCAAGGTGAAA----------------      
cbrenneri     ------------------------TTAAGTAGTGGTGCCGCTCTTATTAG-A--TGAGATAGTAATAAGAGTTGCTCACTACTTAT--------------------------      
cjaponica     TTCAAATTTCAAATTTGTACCTTGTTAAGTAGTGGTGCCGTTCTTATTAA-ATCTCAAAAAGTAATAAGAGCTGTTCATTACTTATCAAGGTAAAGTTTGACCTTTGAG---      
ppacificus     ------------------------ATAAGTAGTGAT-----CTTTTTTAG----CTGAATATCATTA-------TTTTCTAGCTAA------GAAGTTTTGGTATTTCT---      
                               ********* *       ** ***           *  * **        *   *   **                                 
 -----       ------ --------------------------------------  ------------------------------------------------          -----NM_172925
 +++++       ++++++ ++++++++++++++++++++++++++++++++++++++  ++++++++++++++++++++++++++++++++++++++++++++++++          +++++NM_007496
 +++++       ++++++ ++++++++++++++++++++++++++++++++++++++  ++++++++++++++++++++++++++++++++++++++++++++++++          +++++NM_001110231
 +++++       ++++++ ++++++++++++++++++++++++++++++++++++++  ++++++++++++++++++++++++++++++++++++++++++++++++          +++++NM_004119
 +++++       ++++++ ++++++++++++++++++++++++++++++++++++++  ++++++++++++++++++++++++++++++++++++++++++++++++          +++++NM_001110232
 -----       ------ --------------------------------------  ------------------------------------------------          -----NM_007736
 +++++       ++++++ ++++++++++++++++++++++++++++++++++++++  ++++++++++++++++++++++++++++++++++++++++++++++++          +++++NM_001110229
 +++++       ++++++ ++++++++++++++++++++++++++++++++++++++  ++++++++++++++++++++++++++++++++++++++++++++++++          +++++NM_011058
 +++++       ++++++ ++++++++++++++++++++++++++++++++++++++  ++++++++++++++++++++++++++++++++++++++++++++++++          +++++NM_006206
 +++++       ++++++ ++++++++++++++++++++++++++++++++++++++  ++++++++++++++++++++++++++++++++++++++++++++++++          +++++NM_010160
 +++++       ++++++ ++++++++++++++++++++++++++++++++++++++  ++++++++++++++++++++++++++++++++++++++++++++++++          +++++NM_001110228
 +++++       ++++++ ++++++++++++++++++++++++++++++++++++++  ++++++++++++++++++++++++++++++++++++++++++++++++          +++++NM_001110230
 +++++       ++++++ ++++++++++++++++++++++++++++++++++++++  ++++++++++++++++++++++++++++++++++++++++++++++++          +++++NM_001090075
 -----       ------ --------------------------------------  ------------------------------------------------          -----NM_001087789
 -----       ------ --------------------------------------  ------------------------------------------------          -----NM_001079250
 +++++       ++++++ ++++++++++++++++++++++++++++++++++++++  ++++++++++++++++++++++++++++++++++++++++++++++++          +++++NM_001020811
 +++++       ++++++ ++++++++++++++++++++++++++++++++++++++  ++++++++++++++++++++++++++++++++++++++++++++++++          +++++NM_001083316
 +++++       ++++++ ++++++++++++++++++++++++++++++++++++++  ++++++++++++++++++++++++++++++++++++++++++++++++          +++++NM_077435
cbriggsae            .((((( (....((((((((((((((((.((.((((((((((...  ........)))))))))).))))))))))))))))))....)))))).               1.000 -42.20
cremanei     .((.((.(((((( (....(((((.((((((((((.((.((((((((((. .  ........)))))))))).)))))))))))).)))))....)))))))....)).)).     0.998 -41.00
celegans     .......(((((. .....(((((.((((((((((.((..(((((((((. .  ((....)))))))))))..)))))))))))).))))))))))                     0.869 -31.40
cbrenneri                             .((((((((((.((.((((((((((. .  ........)))))))))).)))))))))))).                               1.000 -24.90
cjaponica     .(((((..((((((((.(((((((.((((((((((.((.((((((((((. ...........)))))))))).)))))))))))).)))))))))))))))..))))).        1.000 -40.70
ppacificus                             ..(((((.(((.     .((((((((    (((((........       ..))).))))))      ))))..))).)))))..        0.997 -13.40

cbriggsaechromosome:chrX:5851573:5851664:-1Opposite_strand|Intronic_non-coding|NM_172925|Klhl31 ## Same_strand|Intronic_non-coding|NM_007496|Zfhx3 ## Same_strand|Intronic_coding|NM_004119|FLT3 ## Opposite_strand|Intronic_coding|NM_007736|Col4a5 ## {Repeats: no} ## {MIR: cbr-mir-251}
cremaneichromosome:chrUn:33059029:33059136:1Same_strand|Intronic_coding|NM_074370
celeganschromosome:chrX:11004649:11004740:1intergenic ## {MIR: cel-mir-251}
cbrennerichromosome:chrUn:20061416:20061547:-1Same_strand|Intronic_coding|NM_001104373
cjaponicachromosome:chrUn:181820:181927:1Same_strand|Intronic_coding|NM_001044093
ppacificuschromosome:chrUn:47451400:47451531:-1Opposite_strand|Intronic_coding|NM_001003336


cbr-mir-249

Cloning frequencies
absoluteAF16
cbr-mir-249 3arm2
normalizedAF16
cbr-mir-249 3arm0.005
cbr-mir-249 relative cloning frequencies

block4471 (miRBase cbr-mir-249) [miRNAknown_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBase cbr-mir-2490.001nono0.41/0.4122/22/1.000.0
0.0
2
0
1
0
13
4
3arm
1
nd
0.00
0
21nana
block4471 hairpin
  readsmiRBase family seed
seed     -----------------------------------------------------------------------------------CACAGGA------------------------------------------------     2miR-249
  lencloning frequencies
   AF16
cbr-miR-249     ----------------------------------------------------------------------------------TCACAGGATTTTTGAGTGT--TGC--------------------------------     222
cbriggsae     ATTTGTTATTTTGTGCGCCCTCAATGCTACTAGCAACGCTCAAAAAT-CACTGTACGACAAATGAC-TATAT------TTTGTCACAGGATTTTTGAGTGT--TGCTAGTCGGAGAAGG-------------------      
cremanei     --------------------------------GCAACGCACAAAAGT-TTCTGTGCGACAAATAT--GAAAT------TTTGTCACAGGACTTTTGAGCGT--TGC--------------------------------      
celegans     ----TTGTGTATCTATACTCTTGA-ACGACTAGCAACGCACAAACGTCTTCTGTGCGACAACATCT-GAATG------TTTGTCACAGGACTTTTGAGCGT--TGCCAGTCGAAAGAGGAATTTTTTTATACAA----      
cbrenneri     ACTTTTATTTTTTTGT-CTCTCTGAGCTACTAGCAACGC-TAGAAGTCTACTGTTAGACAGAGTACAGAAAT------TTTGTCACAGGACTTTTGAGCGT--TGCTGGTTAATGAGAGCCTATTTTAGTAATTAGT-      
cjaponica     --TTTTAAATTGTTTTCCTCTCCCTGT--CTAGCGGCGC-CAAAAGATTACTGTGAGGCAAA-----GAAATGGTGAGCTTGTCACAGGACTTTTGAGCGT--TGCTAGTTATAGAGGATGGAATTGTAAGTTTTTGA      
ppacificus     ---------AGCACATACCCTGACTGTGATTAGCAATGC-CACATTT-------------------------------GCTATCACAGGAC---GGAGTGGAATGCC-------------------------------      
                                      **   **  * *                                    * ********     *** *   ***                                      
 ---------------------------------------------------- ------------------ -----      -----------------------  ----------------                   -----NM_178660
 ++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++++ +++++      +++++++++++++++++++++++  ++++++++++++++++                   +++++NM_133381
 ++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++++ +++++      +++++++++++++++++++++++  ++++++++++++++++                   +++++NM_002254
 ++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++++ +++++      +++++++++++++++++++++++  ++++++++++++++++                   +++++NM_001059519
 ++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++++ +++++      +++++++++++++++++++++++  ++++++++++++++++                   +++++NM_024598
 ++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++++ +++++      +++++++++++++++++++++++  ++++++++++++++++                   +++++NM_175804
 ++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++++ +++++      +++++++++++++++++++++++  ++++++++++++++++                   +++++NM_001089427
 ++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++++ +++++      +++++++++++++++++++++++  ++++++++++++++++                   +++++NM_001110788
cbriggsae     ..................(((...(.(.((((((((((((((((((( (.((((..((((((.... .....      )))))))))))))))))))))))  ))))))).).)..)))                        1.000 -42.70
cremanei                                     (((((((.((((((. ((((((..((((((...  .....      )))))))))))))))))).))))  )))                                     1.000 -29.20
celegans         .((((((......(((((.. .(((((.(((((((.((((.(((..((((((((..((((.. ..)))      )))).)))))))).)))).))))  ))).))))).))))).........)))))).         0.994 -43.96
cbrenneri     (((.(((((....... (((((......((((((((((( ((((((((..((((..((((((((......))      ))))))))))))))))).)))))  )))))))....)))))........)))))..)))      0.977 -44.96
cjaponica       ....(((((...((((..(((((((  (((((((((( ((((((....(((((((((...     ..........)))..))))))..)))))).))))  ))))))..)))).))).)))).....)))))....     0.993 -42.12
ppacificus              .(((..(((.(((.((((((.((((((... .....))                               ))))))))))..)   )).)))...))).                                    1.000 -22.80

cbriggsaechromosome:chrX:7892502:7892610:-1Opposite_strand|Intronic_non-coding|NM_178660|Rbms3 ## Same_strand|Intronic_non-coding|NM_133381|Crebbp ## Same_strand|Intronic_coding|NM_002254|KIF3C ## {Repeats: no} ## {MIR: cbr-mir-249}
cremaneichromosome:chrUn:4287040:4287188:1intergenic
celeganschromosome:chrX:3006419:3006538:-1intergenic ## {Repeats: AT_rich 1 28 -1 class=Low_complexity} ## {MIR: cel-mir-249}
cbrennerichromosome:chrUn:1355933:1356059:-1intergenic
cjaponicachromosome:chrUn:20281422:20281547:1intergenic
ppacificuschromosome:chrUn:26943373:26943521:1Opposite_strand|Intronic_coding|NM_136618


cbr-mir-784

Cloning frequencies
absoluteAF16
cbr-mir-784 5arm2
normalizedAF16
cbr-mir-784 5arm0.005
cbr-mir-784 relative cloning frequencies

block4579 (miRBase cbr-mir-784) [miRNAknown_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBase cbr-mir-7840.001nono0.41/0.4321/22/1.000.0
0.0
2
0
1
0
8
5
5arm
1
nd
0.14
2
21nana
block4579 hairpin
  readsmiRBase family seed
seed     ------------------------------GGCACAA-----------------------------------------------------------------------------------     2miR-784
  lencloning frequencies
   AF16
      -----------------------------TGGCACAATACCTGTATGTAG----------------------------------------------------------------------     212
cbr-miR-784     -----------------------------TGGCACAATACCTGTATGTAGA---------------------------------------------------------------------     22-
cbriggsae     --------------------CTACCAAG-TGGCACAATACCTGTATGTAGATAGTG----AAGTAATATTGT-TCTACATACACCTATTGAGCCACCTGGTGG-----------------      
cremanei     ------------ACTTTGCGTTACCGTA-TGGCACAATACTTGCATGTAGAC--------GTGACGTTTGTGATCTACATACATCTATTGAGCCATCCGGTATTCTTGCAAAGT------      
celegans     TCGTATTCTCAGTTTTTCGACGTCCACG-TGGCACAATCTGCGTACGTAGAAAGAT----CAAAAAGTCACT-TCTATGTACAAATGTTGCGCTGCCTGGCACAGTGAATGAATTTATGG      
cbrenneri     -----------------------------TGGCACAAGCGATGAGTTCAACG--------ACGATAACAGTG-TCTCTGAATTCATGTCCAAGTACCA----------------------      
cjaponica     -------------------GTCACGGCGTTGGCACAAAACCTTTTTTTTTAAAGCATTTCATGGAATTTTCC-TTGAAAAGCCTTTA-AGAATGATTTTGAGCAAACGCCGCGAC-----      
ppacificus     -----------------------------TGGCACAAGAAGCGAAAGTGGATAAC-----ATGGAAACATTC-TCTGCAGCTTCTTG-CAATGCAC------------------------      
                                   ********                                    *           *                                        
 +++++                    ++++++++ +++++++++++++++++++++++++++    ++++++++++++ ++++++++++++++++++++++++++++++                 +++++NM_003107
 +++++                    ++++++++ +++++++++++++++++++++++++++    ++++++++++++ ++++++++++++++++++++++++++++++                 +++++NM_011438
 +++++                    ++++++++ +++++++++++++++++++++++++++    ++++++++++++ ++++++++++++++++++++++++++++++                 +++++NM_008638
cbriggsae                         ((((((.( ((((.(((((..(((((((((((((((    ......))))). ))))))))))..))))).))))).))))))                      1.000 -36.20
cremanei                 ((((((((.(((((.( ((((.(((((..((.((((((..        ((.((....)).)))))))).))..))))).))))).)))))....))))))))           1.000 -36.80
celegans     .((((...(((....((((..(((((.( ((((.((((....((((((((((.(((    ......)))..) )))))))))....)))).))))).))).))..)))))))...)))).     0.993 -31.70
cbrenneri                                  .((.((..((.(((((((((..(        (((.......)) ))..)))))))))))....)).)).                           0.988 -14.70
cjaponica                        (((.(((((((.((.(((((......((((((((((.(((((.(((....))) .))))).)).)))) ))))...))))).)).))))))).)))          1.000 -34.70
ppacificus                                  ..(((((((((((....(((((....     (((....))).. ))))).)))))))) ...)))..                             0.998 -20.50

cbriggsaechromosome:chrX:13820037:13820113:-1Same_strand|Intronic_non-coding|NM_003107|SOX4 ## {Repeats: no} ## {MIR: cbr-mir-784}
cremaneichromosome:chrUn:111107627:111107719:-1intergenic
celeganschromosome:chrX:8074853:8074966:-1intergenic ## {MIR: cel-mir-784}
cbrennerichromosome:chrUn:134351040:134351156:-1Opposite_strand|Exonic_coding|NM_068999
cjaponicachromosome:chrUn:142432815:142432908:1Opposite_strand|Intronic_coding|NM_065010
ppacificuschromosome:chrUn:141232002:141232118:-1Opposite_strand|Intronic_coding|NM_001067741


cbr-mir-239b

Cloning frequencies
absoluteAF16
cbr-mir-239b 5arm2
normalizedAF16
cbr-mir-239b 5arm0.005
cbr-mir-239b relative cloning frequencies

block4614 (miRBase cbr-mir-239b) [miRNAknown_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBase cbr-mir-239b0.001nono0.36/0.3821/22/1.000.0
0.0
2
0
1
0
18
1
5arm
1
nd
0.14
2
21nana
block4614 hairpin
  readsmiRBase family seed
seed     -------------------UUGUACU--------------------------------------------------------------------------------------------------     2miR-239a
seed     --------------------UGUACUG-------------------------------------------------------------------------------------------------     0miR-239b
  lencloning frequencies
   AF16
      ------------------TTTGTACTGCACAAA---AGTACTG---------------------------------------------------------------------------------     222
cbr-miR-239b     -------------------TTGTACTGCACAAA---AGTACTG---------------------------------------------------------------------------------     21-
cbriggsae     TAGGACAGACATGCAATTTTTGTACTGCACAAA---AGTACTGACTATTT---------CTCAGCGCTTTTGTCCAGTGCAAGAATGGCAAGAGCTGGTCCATTTTTTTAGGGATTAAACAATT      
cremanei     ------------------TTTGTACTGCACAAA---AGCTCTGACTGCTC-TGATATGGCTCAGCACTTTTGTC-TGTGCAAA-----------------------------------------      
celegans     ------------------TTTGTACTACACAAA---AGTACTGGTCATTTAAGTTGAGGCTCAGCACTTTTGTGGTGTGCAAA-----------------------------------------      
cbrenneri     ------------------TTTGTACTTCACAAG---AGTACTGGCGGTTC-AGGTCCGGCTCAGAACTTTTGTGGGGTGCAAG-----------------------------------------      
cjaponica     -------GCTTGACAATTTTTGTACTACACAAA---AGTTCTGTTCAGCT---TCTATGTACAGCTCGTTTGTCCAGTGCAAAAATGGTTGAGC------------------------------      
ppacificus     ------------------CTTGTACTTGACGCAGTCAACCGTGCCGATCT--------ACGGAAGGAAATTGTC-AGTACAGA-----------------------------------------      
                         *******  **      *    **                   *      ****   ** **                                                 
 --------------------------------------   --------------         ----------------------------------------------------------------------NM_001099298
 ++++++++++++++++++++++++++++++++++++++   ++++++++++++++         ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_077585
cbriggsae     ..((((((...(((.((((((((((((.(((((   ((..((((......         .))))..))))))).)))))))))))).)))....)).)))).......................     1.000 -39.90
cremanei                       .((((((...(((((   ((..((((..(((. ......)))))))..))))))). .)))))).                                              1.000 -17.90
celegans                       .((((((..((((((   (((.((((((.((......))))).))).)))))))))..)))))).                                              1.000 -23.70
cbrenneri                       .((((((..((((((   (((.(((((((... ....)).)).))).)))))))))..)))))).                                              1.000 -30.30
cjaponica            (((..((.(((((((((((..(((((   ....((((.((...   ....)).))))....)))))..))))))))))).))..)))                                   1.000 -28.10
ppacificus                       .((((((.(((((...((..(((((......)        ))))...))...)))) ))))))).                                              0.999 -17.80

cbriggsaechromosome:chrX:15174122:15174233:-1Opposite_strand|Intronic_non-coding|NM_001099298|Scn2a1 ## Same_strand|Intronic_non-coding|NM_077585|Y62H9A.5 ## {Repeats: no} ## {MIR: cbr-mir-239b}
cremaneichromosome:chrUn:26918260:26918411:1intergenic
celeganschromosome:chrX:11791195:11791346:-1intergenic ## {MIR: cel-mir-239b}
cbrennerichromosome:chrUn:34417661:34417812:1intergenic
cjaponicachromosome:chrUn:61792351:61792431:1intergenic
ppacificuschromosome:chrUn:173903385:173903536:1Opposite_strand|Intronic_coding|NM_001047239


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